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Plotting with pepwheel gives interesting output....

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Plotting with pepwheel gives interesting output. pepwheel -turns=8 -send=30 sw:p77837 -auto gives a helical wheel plot but the residues are plotted so every two circles are sat on top of one another.

A) That is the correct answer.

Instead of 3.6 residues per turn, (5 turns in 18 steps) you seem to have a helix with 8 turns in 18 steps (4 in 9).

Try -turns=4 -steps=9 ... but only if you are sure that is the way your helix goes.

I suppose we could play with checking for common factors in pepwheel, but I don't know of any biologically meaningful setting that would cause problems.

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